OCA at 14:13, 18 October 2023

OCA — Wed, 18 Oct 2023 14:13:07 GMT

←Older revision		Revision as of 14:13, 18 October 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8t0j is ~~ON HOLD until Paper~~ Publication	+	==Salmonella Typhimurium ArnD==
		+	<StructureSection load='8t0j' size='340' side='right'caption='[[8t0j]], [[Resolution\|resolution]] 2.59Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8t0j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8T0J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8T0J FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.59Å</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8t0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8t0j OCA], [https://pdbe.org/8t0j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8t0j RCSB], [https://www.ebi.ac.uk/pdbsum/8t0j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8t0j ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ARND_SALTY ARND_SALTY] Catalyzes the deformylation of 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides (Probable).<ref>PMID:11035717</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Covalent modification of lipid A with 4-deoxy-4-amino-l-arabinose (Ara4N) mediates resistance to cationic antimicrobial peptides and polymyxin antibiotics in Gram-negative bacteria. The proteins required for Ara4N biosynthesis are encoded in the pmrE and arnBCADTEF loci, with ArnT ultimately transferring the amino sugar from undecaprenyl-phospho-4-deoxy-4-amino-l-arabinose (C55P-Ara4N) to lipid A. However, Ara4N is N-formylated prior to its transfer to undecaprenyl-phosphate by ArnC, requiring a deformylase activity downstream in the pathway to generate the final C55P-Ara4N donor. Here, we show that deletion of the arnD gene in an Escherichia coli mutant that constitutively expresses the arnBCADTEF operon leads to accumulation of the formylated ArnC product undecaprenyl-phospho-4-deoxy-4-formamido-l-arabinose (C55P-Ara4FN), suggesting that ArnD is the downstream deformylase. Purification of Salmonella typhimurium ArnD (stArnD) shows that it is membrane-associated. We present the crystal structure of stArnD revealing a NodB homology domain structure characteristic of the metal-dependent carbohydrate esterase family 4 (CE4). However, ArnD displays several distinct features: a 44 amino acid insertion, a C-terminal extension in the NodB fold, and sequence divergence in the five motifs that define the CE4 family, suggesting that ArnD represents a new family of carbohydrate esterases. The insertion is responsible for membrane association as its deletion results in a soluble ArnD variant. The active site retains a metal coordination H-H-D triad, and in the presence of Co(2+) or Mn(2+), purified stArnD efficiently deformylates C55P-Ara4FN confirming its role in Ara4N biosynthesis. Mutations D9N and H233Y completely inactivate stArnD implicating these two residues in a metal-assisted acid-base catalytic mechanism.

-	~~Authors~~:	+	Structure and Function of ArnD. A Deformylase Essential for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance.,Munoz-Escudero D, Breazeale SD, Lee M, Guan Z, Raetz CRH, Sousa MC Biochemistry. 2023 Oct 17;62(20):2970-2981. doi: 10.1021/acs.biochem.3c00293. , Epub 2023 Oct 2. PMID:37782650<ref>PMID:37782650</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8t0j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
		+	[[Category: Lee M]]
		+	[[Category: Munoz-Escudero D]]
		+	[[Category: Sousa MC]]

OCA at 04:23, 5 July 2023

OCA — Wed, 05 Jul 2023 04:23:58 GMT

←Older revision		Revision as of 04:23, 5 July 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8t0j is ON HOLD	+	The entry 8t0j is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8t0j" [edit=sysop:move=sysop]

OCA — Wed, 07 Jun 2023 04:30:27 GMT

Protected "8t0j" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:30, 7 June 2023

OCA: New page: '''Unreleased structure''' The entry 8t0j is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 07 Jun 2023 04:30:26 GMT

New page: '''Unreleased structure''' The entry 8t0j is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8t0j is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

8t0j - Revision history

OCA at 14:13, 18 October 2023

OCA at 04:23, 5 July 2023

OCA: Protected "8t0j" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 8t0j is ON HOLD Authors: Description: Category: Unreleased Structures